For breast cancer, we observed limited evidence of associations with rare coding variants in genes proximal to GWAS signals, with 9 genes (PTPN22, PTPN7, MDM4, CASP8, SLC6A18, FOXF2, CTSW, CCDC88C, ZNF404) having SNPs or gene burdens achieving p-values of p<0.05 (Table S6) after correcting for either the number of nearby (+/−100 kb) SNPs (single SNP analyses) or genes (gene burden) for each GWAS index association. Here, PTPN22 is linked to breast cancer.